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## Uses of Class
org.metaqtl.Tree

Packages that use Tree
org.metaqtl |
org.metaqtl.algo |
org.metaqtl.factory |

Uses of Tree in org.metaqtl

Fields in org.metaqtl declared as Tree
`Tree` | `MetaQtlResult.tree` The qtl tree
`Tree` | `QtlPartition.tree` The Qtl tree.

Methods in org.metaqtl that return Tree
`Tree` | `MetaQtlResult.getQtlTree()`

Methods in org.metaqtl with parameters of type Tree
`void` | `MetaQtlResult.setTree(Tree tree)`
`void` | `QtlPartition.setTree(Tree tree)`

Uses of Tree in org.metaqtl.algo

Methods in org.metaqtl.algo that return Tree
`static Tree` | `HClustAlgorithm.CentroidMethod(double[] x, double[] sd)` This method performs a hierarchical clustering of the given data points using a centroid method based on the mahalanobis distance.
`static Tree` | `HClustAlgorithm.run(double[] x, double[] sd)` This method performs a agglomerative clustering of the given data points where `x` is the vector of observed values and `sd` the vector of their standard deviations.
`static Tree` | `HClustAlgorithm.WardMethod(double[] x, double[] sd)` This method performs a hierarchical clustering of the given data points using the Ward's method.

Uses of Tree in org.metaqtl.factory

Methods in org.metaqtl.factory that return Tree
`static Tree` | `TreeFactory.read_newick(java.io.Reader reader)`
`static Tree` | `TreeFactory.read_newick(java.lang.String treeStr)`
`static Tree` | `TreeFactory.read(java.io.Reader reader)`
`static Tree` | `TreeFactory.read(java.lang.String str)`

Methods in org.metaqtl.factory with parameters of type Tree
`static void` | `TreeFactory.write(Tree tree, java.io.OutputStream stream)` This method writes out the given tree `nodes` as an array of `TreeNode` on the given output stream stream.
`static void` | `TreeFactory.write(Tree tree, java.io.PrintWriter writer)` This method writes out the given tree `nodes` as an array of `TreeNode` using the given writer writer.

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